Computational experiments for investigation of the «template»-«artificial receptors» formation kinetics

Abstract

In this paper, the commonly used scheme of ligand receptor interaction was adapted for the first time to modeling of the kinetics «template»-«MIP-receptor» kinetic. The mathematical model that describes the binding process for a monovalent receptor and ligand was created taking into account the conservation of mass criterion and initial ligand receptor interaction scheme. The numerical solution of mentioned mathematical model was carried out using of Runge-Kutta method.That was given an opportunity to investigate the kinetics of noncooperative binding of ligand (template) with MIP-receptor through the carry out of the computational experiment (in MatLab environment).As a result «template»-«MIP-receptor» concentration profiles were obtained for different concentrations of template. It was shown that achieving a balance and, consequently, the formation of complex «template»-«MIP-receptor» is largely depend on the concentration of the template. The most accurate simulation of real experimental conditions in the computational experiment was provided considering dissociation constants that was derived from our previous affinity research of «MIP-receptor»-«template» during surface plasmon resonance experiment with utilizing "Biacore 3000" instrument.This approach significantly increases the probability of the kinetics modeling and makes it possible to optimize the initial experimental conditions (concentration of the ligand and / or receptor) to reduce the time to reach equilibrium. This model can be used to study the kinetics of interaction MIPs that has homogeneous binding sites. These include MIP-nanoparticles synthesized by the method of solid phase synthesis.